Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

“…The two major types of rRNA modifications are 29-O-ribose methylation (Nm) and isomerization of uridine to pseudouridine (C) (Bachellerie et al 2002). The number of modifications in rRNA increases with increasing evolutionary complexity; Escherichia coli has 10 Cs and four Nms, while human rRNA contains more than 90 Cs and 100 Nms (Ofengand and Bakin 1997). In eukaryotes, the site-specificity of these modifications is facilitated by small nucleolar RNAs (snoRNA) which guide the modifying enzymes to their nucleotide targets via a base-pairing mechanism.…”

Section: Introductionmentioning

confidence: 99%

Functional importance of individual rRNA 2′-O-ribose methylations revealed by high-resolution phenotyping

Esguerra

Warringer

2008

RNA

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Ribosomal RNAs contain numerous modifications at specific nucleotides. Despite their evolutionary conservation, the functional role of individual 29-O-ribose methylations in rRNA is not known. A distinct family of small nucleolar RNAs, box C/D snoRNAs, guides the methylating complex to specific rRNA sites. Using a high-resolution phenotyping approach, we characterized 20 box C/D snoRNA gene deletions for altered growth dynamics under a wide array of environmental perturbations, encompassing intraribosomal antibiotics, inhibitors of specific cellular features, as well as general stressors. Ribosome-specific antibiotics generated phenotypes indicating different and long-ranging structural effects of rRNA methylations on the ribosome. For all studied box C/D snoRNA mutants we uncovered phenotypes to extraribosomal growth inhibitors, most frequently reflected in alteration in growth lag (adaptation time). A number of strains were highly pleiotropic and displayed a great number of sensitive phenotypes, e.g., deletion mutants of snR70 and snR71, which both have clear human homologues, and deletion mutants of snR65 and snR68. Our data indicate that individual rRNA ribose methylations can play either distinct or general roles in the workings of the ribosome.

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“…13 and references therein) and LSU rRNAs of human (11) and E. coli (Ref. 14 and references therein) and extensive surveys of pseudouridylation sites in rRNA (6), particularly those from the LSU (15). To these studies can be added a number of early reports, e.g.…”

mentioning

confidence: 99%

Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

Kowalak¹,

Bruenger²,

Crain³

et al. 2000

Journal of Biological Chemistry

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Small subunit (16 S) rRNA from the archaeon Haloferax volcanii, for which sites of modification were previously reported, was examined using mass spectrometry. A census of all modified residues was taken by liquid chromatography/electrospray ionization-mass spectrometry analysis of a total nucleoside digest of the rRNA. Following rRNA hydrolysis by RNase T 1 , accurate molecular mass values of oligonucleotide products were measured using liquid chromatography/electrospray ionization-mass spectrometry and compared with values predicted from the corresponding gene sequence. Three modified nucleosides, distributed over four conserved sites in the decoding region of the molecule, were characterized: 3-(3-amino-3-carboxypropyl)uridine-966, N 6 -methyladenosine-1501, and N 6 ,N 6 -dimethyladenosine-1518 and -1519 (all Escherichia coli numbering). Nucleoside 3-(3-amino-3-carboxypropyl)uridine, previously unknown in rRNA, occurs at a highly conserved site of modification in all three evolutionary domains but for which no structural assignment in archaea has been previously reported. Nucleoside N 6 -methyladenosine, not previously placed in archaeal rRNAs, frequently occurs at the analogous location in eukaryotic small subunit rRNA but not in bacteria. H. volcanii small subunit rRNA appears to reflect the phenotypically low modification level in the Crenarchaeota kingdom and is the only cytoplasmic small subunit rRNA shown to lack pseudouridine.

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Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

Cited by 208 publications

References 45 publications

Genetic aspects of mitochondrial genome evolution

Genetic aspects of mitochondrial genome evolution

Functional importance of individual rRNA 2′-O-ribose methylations revealed by high-resolution phenotyping

Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

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